- BaseX-Talk - mailman.uni-konstanz.de

Re: [basex-talk] BaseX weird error
by halit tiryaki 18 May '18

18 May '18

I'm using the C# driver. but still, it doesn't look like a high level problem. neither a query problem. thats why I didn't post some code snippets. To make sure, I just tried to execute the INSPECT command in the CLI. same exception. Also the db:optimize fails with the same exception, although with a different stacktrace, which I will post below. Altough the race condition point of two processes interfering is a good point, I'm currently having trouble to do anything useful with a session from which a race condition would matter. If, then it must have happened while the import was running along with the other, non-importing process. As I mentioned in the first post, while the import process was still ongoing, the other process already started to have the exception at a very late progress of the import. After the import was done, I was still able to operate on the db as normal, but only with the session in the process which did the long-run import. To restore the second process its session state to normal, I restarted the webapplication, which closes both sessions. After that, I'm no longer to operate on the db. Not even directly from the CLI. Seems it is a sort of a persisted data state which the low level basex code can't handle when trying to reread it into to the memory. I 've already googled around for the same exception in BaseX, seems it was an issue in some older versions too. here the stacktrace when running db:optimize: Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 9.0.2 beta Java: Oracle Corporation, 1.8.0_151 OS: Linux, amd64 Stack Trace: java.lang.ArrayIndexOutOfBoundsException: 52 at org.basex.util.hash.TokenSet.key(TokenSet.java:128) at org.basex.data.Data.name(Data.java:388) at org.basex.io.serial.Serializer.node(Serializer.java:414) at org.basex.io.serial.Serializer.node(Serializer.java:158) at org.basex.io.serial.Serializer.node(Serializer.java:345) at org.basex.io.serial.Serializer.node(Serializer.java:158) at org.basex.io.serial.Serializer.serialize(Serializer.java:109) at org.basex.core.cmd.OptimizeAll$DBParser.parse(OptimizeAll.java:200) at org.basex.build.Builder.parse(Builder.java:77) at org.basex.build.DiskBuilder.build(DiskBuilder.java:77) at org.basex.core.cmd.OptimizeAll.optimizeAll(OptimizeAll.java:122) at org.basex.query.up.primitives.db.DBOptimize.apply(DBOptimize.java:124) at org.basex.query.up.DataUpdates.apply(DataUpdates.java:175) at org.basex.query.up.ContextModifier.apply(ContextModifier.java:120) at org.basex.query.up.Updates.apply(Updates.java:157) at org.basex.query.QueryContext.iter(QueryContext.java:341) at org.basex.query.QueryProcessor.iter(QueryProcessor.java:90) at org.basex.core.cmd.AQuery.query(AQuery.java:92) at org.basex.core.cmd.XQuery.run(XQuery.java:22) at org.basex.core.Command.run(Command.java:257) at org.basex.core.Command.execute(Command.java:93) at org.basex.server.ClientListener.run(ClientListener.java:140) On Wed, May 9, 2018 at 11:45 AM, Alexander Holupirek <alex(a)holupirek.de> wrote: > Hi, > > (please also respond to the list. Others might have suggestions as well > ;-) > > it still would be great if you could provide even more details. For > instance, what programming language do you use?Ideally include a Short, > Self Contained, Correct (Compilable), Example (SSCCE) [1] in order to let > people reproduce the behaviour. > > From a high level perspective, are you sure the sessions do not > interfere? Do you additionally work with BaseXGUI on the database, while > your program is importing? > > Cheers, > Alex > > > [1] http://sscce.org/ > > > On 9. May 2018, at 09:26, halit tiryaki <halit.tiryaki(a)gmail.com> wrote: > > > > hello, thanks for the fast response. > > > > It happened in the process of a large Import. There were two processes > with each a respective Session to BaseX. One process with the Open session > which did the Import was doing fine. The Second process however Starter > having the mentioned exception. After stopping Both processes and > restarting the app, no basex Session is now able to operate normal. > > > > The ArrayIndexOutOfBoundsException already comes in executing the > command INSPECT. > > > > The db-Info returns following: > > > > > > info db: > > Database Properties > > NAME: XXX > > SIZE: 5877 kB > > NODES: 124051 > > DOCUMENTS: 5497 > > BINARIES: 0 > > TIMESTAMP: 2018-05-09T05:20:44.000Z > > UPTODATE: false > > > > Resource Properties > > INPUTPATH: > > INPUTSIZE: 0 b > > INPUTDATE: 2018-05-09T04:32:10.539Z > > > > Indexes > > TEXTINDEX: true > > ATTRINDEX: true > > TOKENINDEX: false > > FTINDEX: false > > TEXTINCLUDE: /item_User/node()/User:Email > > ATTRINCLUDE: /item_UserImage/node()/UserImage:Id > > TOKENINCLUDE: > > FTINCLUDE: /item_XXX/node()/XXX:[german] > > LANGUAGE: English > > STEMMING: false > > CASESENS: false > > DIACRITICS: false > > STOPWORDS: > > UPDINDEX: true > > AUTOOPTIMIZE: false > > MAXCATS: 100 > > MAXLEN: 96 > > SPLITSIZE: 0 > > Alexander Holupirek <alex(a)holupirek.de> schrieb am Mi., 9. Mai 2018 > 08:44: > > Hi, > > > > could you please provide some more details? > > The best would be a reproducible example. > > > > Thanks, > > Alex > > > > > > > On 9. May 2018, at 06:50, halit tiryaki <halit.tiryaki(a)gmail.com> > wrote: > > > > > > Hello, > > > > > > got a serious problem here. any ideas? thanks > > > > > > Improper use? Potential bug? Your feedback is welcome: > > > Contact: basex-talk(a)mailman.uni-konstanz.de > > > Version: BaseX 9.0.2 beta > > > Java: Oracle Corporation, 1.8.0_151 > > > OS: Linux, amd64 > > > Stack Trace: > > > java.lang.ArrayIndexOutOfBoundsException: 4288 > > > at org.basex.io.random.TableDiskAccess.read1(TableDiskAccess.java:151) > > > at org.basex.data.Data.kind(Data.java:294) > > > at org.basex.query.value.node.DBNode$4.next(DBNode.java:332) > > > at org.basex.query.value.node.DBNode$4.next(DBNode.java:323) > > > at org.basex.query.expr.path.IterStep$1.next(IterStep.java:38) > > > at org.basex.query.expr.path.IterStep$1.next(IterStep.java:32) > > > at org.basex.query.QueryContext.next(QueryContext.java:392) > > > at org.basex.query.expr.path.IterPath$1.next(IterPath.java:50) > > > at org.basex.query.expr.path.IterPath$1.next(IterPath.java:34) > > > at org.basex.query.expr.ParseExpr.item(ParseExpr.java:58) > > > at org.basex.query.expr.ParseExpr.atomItem(ParseExpr.java:84) > > > at org.basex.query.func.fn.FnConcat.item(FnConcat.java:20) > > > at org.basex.query.expr.ParseExpr.value(ParseExpr.java:71) > > > at org.basex.query.expr.gflwor.Let$LetEval.next(Let.java:177) > > > at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) > > > at org.basex.query.expr.path.CachedPath.nodeIter(CachedPath.java:36) > > > at org.basex.query.expr.path.AxisPath.iter(AxisPath.java:69) > > > at org.basex.query.expr.gflwor.For$1.next(For.java:107) > > > at org.basex.query.expr.gflwor.OrderBy$1.sort(OrderBy.java:73) > > > at org.basex.query.expr.gflwor.OrderBy$1.next(OrderBy.java:54) > > > at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) > > > at org.basex.query.expr.gflwor.Let$LetEval.next(Let.java:177) > > > at org.basex.query.expr.gflwor.GFLWOR$1.next(GFLWOR.java:87) > > > at org.basex.query.QueryContext.next(QueryContext.java:392) > > > at org.basex.query.scope.MainModule$1.next(MainModule.java:122) > > > at org.basex.core.cmd.AQuery.query(AQuery.java:94) > > > at org.basex.core.cmd.XQuery.run(XQuery.java:22) > > > at org.basex.core.Command.run(Command.java:257) > > > at org.basex.core.Command.execute(Command.java:93) > > > at org.basex.server.ClientListener.run(ClientListener.java:140) > > > >

2 6

Documentation inquiries
by Marco Lettere 16 May '18

16 May '18

Hi all, investigating the new features tagged 9.x, I discovered a lot of great stuff. I have teo smaller questions ... I'd like to know whether the new "-c flag" for the Basex Http Server in [1] means that one can request a script of commands to be executed once at startup of the server. Is there a way to do something equivalent also at server shutdown? In [2] with the new Service it is said that one could write jobs.xml file inside the database directory. I couldn't find the specification of the syntax of this file anywhere. Do you have some hints? Bye, Marco. [1] http://docs.basex.org/wiki/Command-Line_Options#HTTP_Server [2] http://docs.basex.org/wiki/Jobs_Module#Services

2 1

How to use BaseX on MacBook? (Urgent!)
by Ben Engbers 16 May '18

16 May '18

Hi, If we manage to install BaseX on a MacBook, chances are great that we will use BaseX dor our final project. I know how to install BaseX on linux but I have no experience with Apple. My fellow-students know how to use applications but don't know how to deal with java-applications. My question is if BaseX can be used on a MacBook. If so, where can I find instructions? Cheers, Ben Engbers

3 2

Test Failure From Current Source, Failure to Run GUI from Eclipse
by Eliot Kimber 15 May '18

15 May '18

I thought I would see if I could add the Xerces grammar caching to BaseX, at least to see if it improved things for DITA loading. I've updated my fork of the basex project to the current version in github. Using the master branch as the basis for my local feature branch and with no modified files, I get one failing test from "mvn test": Failed tests: FnTest.sum:91->AdvancedQueryTest.error:78 Query did not fail: sum(1, 'x') [E] Error: err:FORG0006 [F] 1 Tests run: 1578, Failures: 1, Errors: 0, Skipped: 5 I'm also not able to run the BaseXGUI class using an Eclipse run configuration per the documentation on the BaseX site. I get A bunch of messages about things missing from English.lang: /lang/English.lang not found. English.lang: 'port' is missing ... lots more English.lang: 'h_no_html_parser' is missing Then this fatal error: Image not found: /img/text_xml.png at org.basex.util.Util.stack(Util.java:224) at org.basex.gui.layout.BaseXImages.url(BaseXImages.java:125) at org.basex.gui.layout.BaseXImages.get(BaseXImages.java:62) at org.basex.gui.layout.BaseXImages.icon(BaseXImages.java:109) at org.basex.gui.layout.BaseXImages.<clinit>(BaseXImages.java:34) at org.basex.gui.GUIMacOSX.addDockIcon(GUIMacOSX.java:84) at org.basex.gui.GUIMacOSX.<init>(GUIMacOSX.java:60) at org.basex.BaseXGUI.<init>(BaseXGUI.java:58) at org.basex.BaseXGUI.main(BaseXGUI.java:39) Exception in thread "main" java.lang.ExceptionInInitializerError at org.basex.gui.GUIMacOSX.addDockIcon(GUIMacOSX.java:84) at org.basex.gui.GUIMacOSX.<init>(GUIMacOSX.java:60) at org.basex.BaseXGUI.<init>(BaseXGUI.java:58) at org.basex.BaseXGUI.main(BaseXGUI.java:39) Caused by: java.lang.IllegalArgumentException: input == null! at javax.imageio.ImageIO.read(ImageIO.java:1388) at org.basex.gui.layout.BaseXImages.get(BaseXImages.java:72) at org.basex.gui.layout.BaseXImages.get(BaseXImages.java:62) at org.basex.gui.layout.BaseXImages.icon(BaseXImages.java:109) at org.basex.gui.layout.BaseXImages.<clinit>(BaseXImages.java:34) ... 4 more I suspect it's something very simple but no idea what it might be. Thanks, Eliot -- Eliot Kimber http://contrext.com

2 1

"Database path [...] yields more than one document" with static file
by Andreas Mixich 14 May '18

14 May '18

Hi, during development I sometimes use the static file, that contains my database: declare variable $app:db := doc('file:/S:/Users/dev/Eigene%20Projekte/codingcookbook/src/data/dbsample.xml'); So far, it went without problems, but today something very strange happened: [basex:doc] Database path 'file:/S:/Users/dev/Eigene%20Projekte /codingcookbook/src/data/dbsample.xml' yields more than one document. Now I checked the file in question. It is well formed and has a single document-root. One thing may be interesting to note: When I imported that file into a BaseX database, a few days ago, it resulted in that document being in the database twice. Once as it was on disk and once it contained only a single comment, that I had in the file after the <?xml ...> prolog. I moved the comment to another place, even removed it, just to make sure, but the error persists, when trying to load the file from disk via `doc()` Error: Stopped at S:/Users/dev/Eigene Projekte/xquery-appframework/src/lib/app.xqm, 37/32: [basex:doc] Database path 'file:/S:/Users/dev/Eigene%20Projekte/codingcookbook/src/data/dbsample.xml' yields more than one document. Optimized Query: declare variable $app:db as item()* := doc("file:/S:/Users/dev/Eigene%20Projekte/codingcookbook/src/data/dbsample.xml"); declare function local:autoComplete($search_489 as xs:string, $record-name_490 as xs:string, $places_491 as element()*, $title_492, $categories_493) as element(container)* { for $var_494 in $app:db/descendant-or-self::node()/node()[({http://www.w3.org/1999/xhtml}name = $record-name_490)]/$places_491 where $var_494/text()[. contains text { $search_489 } using fuzzy using stemming using language 'English'] return element Q{dev:intermediatexml:unstable}container { (element Q{dev:intermediatexml:unstable}item { ($var_494/text()) }, element Q{dev:intermediatexml:unstable}title { ($var_494/preceding::node()[1]/node()[(name() = $title_492)]/text()) }, element Q{dev:intermediatexml:unstable}categories { ($var_494/preceding::node()[1]/node()[(name() = $categories_493)]/text()) }, element Q{dev:intermediatexml:unstable}id { (($var_494/parent::{http://www.w3.org/1999/xhtml}entry/@xml:id ! string())) }) } }; local:autoComplete("nested", "cb:entry", ((dc:subject union dc:title union {http://www.w3.org/1999/xhtml}question)), "dc:title", "cb:categories") Query: declare base-uri "file:///S:/Users/dev/Eigene%20Projekte/xquery-appframework/src/"; import module namespace app = "dev:app:unstable" at "lib/app.xqm"; declare default element namespace "http://www.w3.org/1999/xhtml"; declare namespace cb = "http://codeblocker.org/ns/codingcookbook/1.0/"; declare namespace dc = "http://purl.org/dc/elements/1.1/"; declare namespace itx = "dev:intermediatexml:unstable"; declare function local:autoComplete( $search as xs:string, $record-name as xs:string, $places as element()*, $title, $categories ) as element(Q{dev:intermediatexml:unstable}container)* { for $var in $app:db//node()[name=$record-name]/$places where $var/text()[. contains text {$search} using stemming using fuzzy] return <itx:container> <itx:item>{$var/text()}</itx:item> <itx:title>{$var/preceding::node()[1]/node()[name()=$title]/text()}</itx:title> <itx:categories>{$var/preceding::node()[1]/node()[name()=$categories]/text()}</itx:categories> <itx:id>{$var/parent::entry/@xml:id/string()}</itx:id> </itx:container> }; local:autoComplete("nested","cb:entry",(dc:subject|dc:title|question),"dc:title","cb:categories") -- Goody Bye, Minden jót, Mit freundlichen Grüßen, Andreas Mixich

2 1

Duplicate declaration of static variable
by Andreas Mixich 14 May '18

14 May '18

Hi, when loading my RESTXQ app I get this: Stopped at C:/Users/dev/.jetty/webapps/basex/fwdev/lib/account.xqm, 20/18: [XQST0049] Duplicate declaration of static variable $acc:last-visited. dev@mambo ~/.jetty/webapps/basex $ grep -R --include="*.*" "\$acc\:last-visited" . ./fwdev/lib/account.xqm:declare variable $acc:last-visited as xs:dateTime? external := (); As it seems, there is no other declaration of the variable in the whole project. What could that be? -- Goody Bye, Minden jót, Mit freundlichen Grüßen, Andreas Mixich

2 1

Re: [basex-talk] 9.0.1: High Memory Usage Loading Docs Via GUI
by Eliot Kimber 14 May '18

14 May '18

Follow up--I tried giving BaseX the full 16GB of RAM and it still ultimately locked up with the memory meter showing 13GB. I'm thinking this must be some kind of memory leak. I tried importing the DITA Open Toolkit's documentation source and that worked fine with the max memory being about 2.5GB, but it's only about 250 topics. Cheers, E. -- Eliot Kimber http://contrext.com On 5/3/18, 4:59 PM, "Eliot Kimber" <basex-talk-bounces(a)mailman.uni-konstanz.de on behalf of ekimber(a)contrext.com> wrote: In the context of trying to do fun things with DITA docs in BaseX I downloaded the latest BaseX (9.0.1) and tried creating a new database and loading docs into it using the BaseX GUI. This is on macOS 10.13.4 with 16GB of hardware RAM available. My corpus is about 4000 DITA topics totaling about 30MB on disk. They are all in a single directory (not my decision) if that matters. Using the "parse DTDs" option and default indexing options (no token or full text indexes) I'm finding that even with 12GB of RAM allocated to the JVM the memory usage during load will eventually go to 12GB, at which point the processing appears to stop (that is, whatever I set the max memory to, when it's reached, things stop but I only got out of memory errors when I had much lower settings, like the default 2GB). I'm currently running a test with 14GB allocated and it is continuing but it does go to 12GB occasionally (watching the memory display on the Add progress panel). No individual file is that big--the biggest is 150K and typical is 30K or smaller. I wouldn't expect BaseX to have this kind of memory problem so I'm wondering if maybe there's an issue with memory on macOS or with DITA documents in particular (the DITA DTDs are notoriously large)? Should I expect BaseX to be able to load this kind of corpus with 14GB of RAM? Cheers, E. -- Eliot Kimber http://contrext.com

2 7

Unexpected unary lookup result
by Sebastian Zimmer 14 May '18

14 May '18

Hi, I have this script where I use the lookup operator to perform a unary lookup: xquery version "3.1"; declare namespace array = "http://www.w3.org/2005/xpath-functions/array"; let $array := [] return ( empty($array!?*), (: returns false :) empty( for $i in 1 to array:size($array) return $array($i) ) (: returns true :) ) I'm curious that the first expression returns false even though it should be equivalent to the second expression, if I read the XQuery spec [1] right: If the context item is an array: If theKeySpecifier <https://www.w3.org/TR/2017/REC-xquery-31-20170321/#doc-xquery31-KeySpecifier>is a wildcard ("|*|"), theUnaryLookup <https://www.w3.org/TR/2017/REC-xquery-31-20170321/#doc-xquery31-UnaryLookup>operator is equivalent to the following expression: for $k in 1 to array:size(.) return .($k) But maybe I'm missing something. I'd be glad if you could help. Best regards, Sebastian Zimmer [1] https://www.w3.org/TR/2017/REC-xquery-31-20170321/#id-unary-lookup -- Sebastian Zimmer sebastian.zimmer(a)uni-koeln.de <mailto:sebastian.zimmer@uni-koeln.de> CCeH Logo <http://cceh.uni-koeln.de> Cologne Center for eHumanities <http://cceh.uni-koeln.de> DH Center at the University of Cologne Twitter Logo <https://twitter.com/CCeHum>@CCeHum <https://twitter.com/CCeHum>

3 6

BaseX weird error
by halit tiryaki 09 May '18

09 May '18

Hello, got a serious problem here. any ideas? thanks Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 9.0.2 beta Java: Oracle Corporation, 1.8.0_151 OS: Linux, amd64 Stack Trace: java.lang.ArrayIndexOutOfBoundsException: 4288 at org.basex.io.random.TableDiskAccess.read1(TableDiskAccess.java:151) at org.basex.data.Data.kind(Data.java:294) at org.basex.query.value.node.DBNode$4.next(DBNode.java:332) at org.basex.query.value.node.DBNode$4.next(DBNode.java:323) at org.basex.query.expr.path.IterStep$1.next(IterStep.java:38) at org.basex.query.expr.path.IterStep$1.next(IterStep.java:32) at org.basex.query.QueryContext.next(QueryContext.java:392) at org.basex.query.expr.path.IterPath$1.next(IterPath.java:50) at org.basex.query.expr.path.IterPath$1.next(IterPath.java:34) at org.basex.query.expr.ParseExpr.item(ParseExpr.java:58) at org.basex.query.expr.ParseExpr.atomItem(ParseExpr.java:84) at org.basex.query.func.fn.FnConcat.item(FnConcat.java:20) at org.basex.query.expr.ParseExpr.value(ParseExpr.java:71) at org.basex.query.expr.gflwor.Let$LetEval.next(Let.java:177) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.expr.path.CachedPath.nodeIter(CachedPath.java:36) at org.basex.query.expr.path.AxisPath.iter(AxisPath.java:69) at org.basex.query.expr.gflwor.For$1.next(For.java:107) at org.basex.query.expr.gflwor.OrderBy$1.sort(OrderBy.java:73) at org.basex.query.expr.gflwor.OrderBy$1.next(OrderBy.java:54) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:72) at org.basex.query.expr.gflwor.Let$LetEval.next(Let.java:177) at org.basex.query.expr.gflwor.GFLWOR$1.next(GFLWOR.java:87) at org.basex.query.QueryContext.next(QueryContext.java:392) at org.basex.query.scope.MainModule$1.next(MainModule.java:122) at org.basex.core.cmd.AQuery.query(AQuery.java:94) at org.basex.core.cmd.XQuery.run(XQuery.java:22) at org.basex.core.Command.run(Command.java:257) at org.basex.core.Command.execute(Command.java:93) at org.basex.server.ClientListener.run(ClientListener.java:140)

2 1

Distributed XML processing on Apache Spark
by Andrey Yatsuk 08 May '18

08 May '18

Hello. Briefing: I want to implement distributed work with BaseX in Hadoop using Apache Spark. Data processing will be divided into the following stages: 1) Splitting XML into chunks 2) Parallel parsing and filling the database 3) Executing queries to make the table (Apache Spark Dataset<Row>) Stage 1 is a simple algorithmic problem. It will compose a HashMap of (ChunkNumber -> List<Xml_Path>). Each chunk contains no more than 128 MB of data. Step 2. On each node of the cluster will initialized a standalone instance of BaseX. Every instance of BaseX will recieve files / lines from HDFS to the input. A xml database of each chunk as result will be serialized to HDFS. Stage 3. When the request of a query is received, each xml database will be sequentially deserialized to apply the query. A table will be composed from the result. Questions: 1) Send data from HDFS to embedded BaseX: 1.1) Does BaseX support reading data by schemed URI, e.g. `hdfs://home/user/file.xml`? 1.2) Can I send XML from RAM to BaseX? 1.3) Can I send XML lines (line by line) to BaseX? 2) Can I get a database in ram to serialize it in HDFS? 3.1) Do I need to store XML in a persistent path to query it in the future? 3.2) When executing a query on XML in HDFS, can I read it line by line if BaseX does not know how to work with it directly? Best regards, Andrei Iatsuk.

2 1